Previous studies have shown that altered methylation patterns are highly heritable over multiple generations and can be incorporated into a quantitative analysis of variation (Vaughn et al. 2007 PLoS Biol. 2007 July; 5(7):e174. Epub 2007 Jun. 19.; Zhang Science. 2008 Apr. 25; 320(5875):489-92. doi: 10.1126/science.1153996.; Cortijo et al., Science. 2014 Mar. 7; 343(6175):1145-8. doi: 10.1126/science.1248127. Epub 2014 Feb. 6.). Earlier studies of methylation changes in Arabidopsis suggest amenability of the epigenome to recurrent selection and also suggest that it is feasible to establish new and stable epigenetic states (F. Johannes et al. PLoS Genet. 5, e1000530 (2009); F. Roux et al. Genetics 188, 1015 (2011). Manipulation of the Arabidopsis met1 and ddmt mutants has allowed the creation of epi-RIL populations that show both heritability of novel methylation patterning and epiallelic segregation, underscoring the likely influence of epigenomic variation in plant adaptation (F. Roux et al. Genetics 188, 1015 (2011)). In natural populations, a large proportion of the epiallelic variation detected in Arabidopsis is found as CpG methylation within gene-rich regions of the genome (C. Becker et al. Nature 480, 245 (2011), R. J. Schmitz et al. Science 334, 369 (2011). Induction of traits that exhibit cytoplasmic inheritance (Redei Mutat. Res. 18, 149-162, 1973; Sandhu et al. Proc Natl Acad Sci USA. 104:1766-70, 2007) or that exhibit nuclear inheritance by suppression of the MSH1 gene has also been reported (WO 2012/151254; Xu et al. Plant Physiol. Vol. 159:711-720, 2012). Genetic hemicomplementation experiments, wherein plastidic MSH1 was suppressed in the presence of mitochondrial-targeted MSH1, show that suppression of MSH1 in the plastid triggers a variegation phenotype (Xu et al. Plant Physiol. Vol. 159:711-720, 2012).